library(tibble)
mapping_data= as.tibble(sample_data(final_ps_NO_Outlier_NO_singelton))
mapping_data$Sampling_day= as.factor(mapping_data$Sampling_day)
mapping_data
## # A tibble: 170 x 17
##    SampleID plate_number sample_type Fish_ID Sample_Number Fish_ID_sample_…
##       <int>        <int> <fct>         <int>         <int> <fct>           
##  1      100            2 catfish_po…   15454             3 15454-3         
##  2      101            2 catfish_po…   15454             7 15454-7         
##  3      102            2 catfish_po…   15455             1 15455-1         
##  4      103            2 catfish_po…   15455             2 15455-2         
##  5      104            2 catfish_po…   15455             3 15455-3         
##  6      105            2 catfish_po…   15455             5 15455-5         
##  7      106            2 catfish_po…   15455             6 15455-6         
##  8      107            2 catfish_po…   15455             7 15455-7         
##  9      108            2 catfish_po…   15456             5 15456-5         
## 10      109            2 catfish_po…   15456             7 15456-7         
## # … with 160 more rows, and 11 more variables: Sampling_day <fct>, date <fct>,
## #   tank2 <fct>, tank <fct>, temperature <dbl>, start_length <dbl>,
## #   start_weight <dbl>, end_length <int>, end_weight <dbl>,
## #   change_In_Length <dbl>, change_In_weight <dbl>

#Outlier 98 I remove the sample 98 because it was the only Outlier

#change in weight and Length

## Using Sampling_day, tank as id variables
## Using Sampling_day, tank as id variables

#Beta Diversity (unifrac), Alpha Diversity (rarefy @ 1044) and Abundance

## 
## Call:
## adonis(formula = final_ps_NO_Outlier_NO_singelton_bray ~ tank +      Sampling_day + Fish_ID, data = sampledf) 
## 
## Permutation: free
## Number of permutations: 999
## 
## Terms added sequentially (first to last)
## 
##               Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)    
## tank           3     1.690 0.56345  2.7447 0.04231  0.001 ***
## Sampling_day   6     5.016 0.83594  4.0721 0.12556  0.001 ***
## Fish_ID        1     0.600 0.60044  2.9249 0.01503  0.008 ** 
## Residuals    159    32.640 0.20529         0.81710           
## Total        169    39.947                 1.00000           
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

#observed bacterial species for each Fish (15351,15352 etc) over time

library(phyloseq)
library(devtools)
#remotes::install_github("vmikk/metagMisc")

library("metagMisc")
tank_phyloseqs_proportions= phyloseq_sep_variable(final_ps_NO_Outlier_NO_singelton_Proportions, "tank")
#tank1c
tank_phyloseqs_proportions$`1c`
## phyloseq-class experiment-level object
## otu_table()   OTU Table:         [ 1403 taxa and 39 samples ]
## sample_data() Sample Data:       [ 39 samples by 17 sample variables ]
## tax_table()   Taxonomy Table:    [ 1403 taxa by 7 taxonomic ranks ]
## phy_tree()    Phylogenetic Tree: [ 1403 tips and 1402 internal nodes ]
#tank2c
tank_phyloseqs_proportions$`2c`
## phyloseq-class experiment-level object
## otu_table()   OTU Table:         [ 2268 taxa and 45 samples ]
## sample_data() Sample Data:       [ 45 samples by 17 sample variables ]
## tax_table()   Taxonomy Table:    [ 2268 taxa by 7 taxonomic ranks ]
## phy_tree()    Phylogenetic Tree: [ 2268 tips and 2267 internal nodes ]
#tank3b
tank_phyloseqs_proportions$`3b`
## phyloseq-class experiment-level object
## otu_table()   OTU Table:         [ 1788 taxa and 43 samples ]
## sample_data() Sample Data:       [ 43 samples by 17 sample variables ]
## tax_table()   Taxonomy Table:    [ 1788 taxa by 7 taxonomic ranks ]
## phy_tree()    Phylogenetic Tree: [ 1788 tips and 1787 internal nodes ]
#tank3c
tank_phyloseqs_proportions$`3c`
## phyloseq-class experiment-level object
## otu_table()   OTU Table:         [ 1021 taxa and 43 samples ]
## sample_data() Sample Data:       [ 43 samples by 17 sample variables ]
## tax_table()   Taxonomy Table:    [ 1021 taxa by 7 taxonomic ranks ]
## phy_tree()    Phylogenetic Tree: [ 1021 tips and 1020 internal nodes ]

##tank 1c # Beta Diversity and Hierachical clustering tank 1c & similarity percentages (SIMPER)

## 
## Call:
## adonis(formula = final_ps_bray ~ Sampling_day + Fish_ID, data = sampledf) 
## 
## Permutation: free
## Number of permutations: 999
## 
## Terms added sequentially (first to last)
## 
##              Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)    
## Sampling_day  5    2.7200 0.54401  1.8302 0.21512  0.001 ***
## Fish_ID       1    0.4123 0.41232  1.3872 0.03261  0.051 .  
## Residuals    32    9.5119 0.29725         0.75227           
## Total        38   12.6442                 1.00000           
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##  [1] 0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  1  1  1  1  3  3  3  3  3  3 
## [26] 3  5  5  5  5  5  5  5  7  7  7  7  7  21
## Levels: 0 1 3 5 7 21

## cumulative contributions of most influential species:
## 
## $`0_3`
##     ASV_1     ASV_2     ASV_4     ASV_5     ASV_8    ASV_14    ASV_13     ASV_6 
## 0.2249376 0.3417685 0.4204450 0.4933250 0.5198915 0.5453851 0.5685554 0.5897862 
##    ASV_17     ASV_7    ASV_22    ASV_10    ASV_29    ASV_52    ASV_49    ASV_42 
## 0.6085536 0.6233455 0.6372845 0.6505314 0.6607156 0.6708248 0.6806765 0.6897858 
##    ASV_21    ASV_32 
## 0.6980445 0.7056588 
## 
## $`0_5`
##     ASV_1     ASV_2     ASV_4    ASV_17     ASV_6    ASV_48     ASV_7     ASV_9 
## 0.2284310 0.3676688 0.4527429 0.4793300 0.5021091 0.5235319 0.5396229 0.5547443 
##    ASV_22    ASV_10    ASV_38    ASV_14    ASV_29    ASV_49    ASV_42    ASV_21 
## 0.5697497 0.5845196 0.5986399 0.6126710 0.6239597 0.6346149 0.6445139 0.6534327 
##    ASV_32    ASV_24     ASV_5    ASV_28    ASV_23    ASV_80    ASV_39 
## 0.6618173 0.6692423 0.6760344 0.6825435 0.6889924 0.6953535 0.7016836 
## 
## $`0_7`
##     ASV_1     ASV_2     ASV_4     ASV_6     ASV_7    ASV_22    ASV_14    ASV_10 
## 0.2895727 0.3900952 0.4641156 0.4841549 0.4982357 0.5114955 0.5240067 0.5365030 
##    ASV_33    ASV_55    ASV_29    ASV_49    ASV_57    ASV_42   ASV_303   ASV_304 
## 0.5469633 0.5570035 0.5666488 0.5759278 0.5849490 0.5935800 0.6020140 0.6104038 
##    ASV_61   ASV_315    ASV_21    ASV_63   ASV_331   ASV_334    ASV_32   ASV_345 
## 0.6185559 0.6267021 0.6344754 0.6419381 0.6493981 0.6568361 0.6640847 0.6711905 
##   ASV_346   ASV_347   ASV_352   ASV_354   ASV_332 
## 0.6782521 0.6852916 0.6921982 0.6990827 0.7058122 
## 
## $`0_1`
##     ASV_1     ASV_2    ASV_30     ASV_4     ASV_5    ASV_18     ASV_3     ASV_6 
## 0.2293697 0.3519091 0.4517204 0.5312088 0.5796240 0.6165966 0.6437652 0.6637149 
##    ASV_10    ASV_14     ASV_7 
## 0.6806650 0.6966248 0.7113071 
## 
## $`0_21`
##     ASV_1     ASV_2     ASV_4    ASV_38    ASV_54     ASV_3     ASV_6     ASV_7 
## 0.2703207 0.3939574 0.4957436 0.5579093 0.5898708 0.6183098 0.6460004 0.6654713 
##    ASV_22    ASV_14 
## 0.6836646 0.7009467 
## 
## $`3_5`
##     ASV_1     ASV_2     ASV_5    ASV_17     ASV_8    ASV_13    ASV_48    ASV_14 
## 0.2080986 0.3516990 0.4358519 0.4798221 0.5105480 0.5367477 0.5601299 0.5802764 
##    ASV_38     ASV_9    ASV_52    ASV_91    ASV_27    ASV_60    ASV_80    ASV_16 
## 0.5956908 0.6096687 0.6215892 0.6290171 0.6360618 0.6430169 0.6499643 0.6565571 
##     ASV_3   ASV_443    ASV_30   ASV_120   ASV_426    ASV_94   ASV_715    ASV_12 
## 0.6631219 0.6691470 0.6751359 0.6809289 0.6864729 0.6919272 0.6973596 0.7027128 
## 
## $`3_7`
##     ASV_1     ASV_2     ASV_5     ASV_8    ASV_13    ASV_17    ASV_14    ASV_33 
## 0.2884237 0.3805331 0.4528457 0.4791457 0.5015196 0.5200789 0.5371879 0.5483895 
##    ASV_55    ASV_52    ASV_57   ASV_303   ASV_304    ASV_61   ASV_315    ASV_63 
## 0.5592823 0.5694858 0.5793229 0.5883675 0.5973646 0.6062400 0.6149759 0.6230640 
##   ASV_331   ASV_334   ASV_345   ASV_346   ASV_347   ASV_352   ASV_354   ASV_332 
## 0.6310641 0.6390404 0.6466606 0.6542333 0.6617823 0.6691889 0.6765717 0.6837884 
##    ASV_16   ASV_373    ASV_71 
## 0.6907236 0.6976554 0.7045728 
## 
## $`3_1`
##     ASV_1     ASV_2    ASV_30     ASV_5    ASV_18     ASV_3     ASV_8    ASV_14 
## 0.2252776 0.3496842 0.4534481 0.5571988 0.5938589 0.6213485 0.6479664 0.6726263 
##    ASV_13    ASV_17 
## 0.6961268 0.7175684 
## 
## $`3_21`
##     ASV_1     ASV_2     ASV_5    ASV_38     ASV_8    ASV_54    ASV_13     ASV_3 
## 0.2509058 0.4014086 0.5007299 0.5669712 0.6028819 0.6369388 0.6674926 0.6962123 
##    ASV_17 
## 0.7215537 
## 
## $`5_7`
##     ASV_1     ASV_2    ASV_17    ASV_48    ASV_38    ASV_33     ASV_9    ASV_55 
## 0.2942730 0.4044326 0.4320884 0.4548479 0.4697171 0.4839792 0.4978134 0.5101392 
##    ASV_57   ASV_303   ASV_304    ASV_61   ASV_315    ASV_63   ASV_331   ASV_334 
## 0.5212655 0.5314584 0.5415978 0.5516048 0.5614500 0.5705944 0.5796102 0.5885992 
##   ASV_345   ASV_346   ASV_347   ASV_352   ASV_354   ASV_332   ASV_373    ASV_71 
## 0.5971869 0.6057212 0.6142287 0.6225756 0.6308958 0.6390288 0.6468407 0.6546351 
##    ASV_70   ASV_383    ASV_76   ASV_398    ASV_83    ASV_80   ASV_412 
## 0.6623669 0.6698578 0.6772537 0.6844236 0.6914426 0.6982794 0.7050747 
## 
## $`5_1`
##     ASV_1     ASV_2    ASV_30     ASV_5    ASV_18     ASV_3    ASV_17    ASV_48 
## 0.2266033 0.3721551 0.4796750 0.5314437 0.5705545 0.6001647 0.6290179 0.6506339 
##     ASV_9    ASV_38    ASV_10    ASV_14 
## 0.6687566 0.6830042 0.6959190 0.7080454 
## 
## $`5_21`
##     ASV_2     ASV_1    ASV_38    ASV_17    ASV_54    ASV_48     ASV_3     ASV_9 
## 0.2404446 0.4231687 0.4883950 0.5326290 0.5703187 0.6064007 0.6423362 0.6635767 
##    ASV_80   ASV_443   ASV_696   ASV_120 
## 0.6742907 0.6835867 0.6928566 0.7017945 
## 
## $`7_1`
##     ASV_1     ASV_2    ASV_30     ASV_5    ASV_18     ASV_3    ASV_10    ASV_14 
## 0.2883433 0.3932031 0.4870067 0.5323112 0.5663341 0.5915973 0.6028901 0.6137749 
##    ASV_33    ASV_55    ASV_57   ASV_303   ASV_304    ASV_61   ASV_315    ASV_63 
## 0.6246440 0.6347531 0.6438363 0.6523283 0.6607757 0.6689837 0.6771860 0.6846999 
##   ASV_331   ASV_334   ASV_345 
## 0.6922112 0.6997002 0.7068549 
## 
## $`7_21`
##     ASV_1     ASV_2    ASV_38    ASV_54     ASV_3    ASV_33    ASV_55    ASV_57 
## 0.3105460 0.4776467 0.5388606 0.5703327 0.5976816 0.6118157 0.6254014 0.6376082 
##   ASV_303   ASV_304    ASV_61   ASV_315    ASV_63   ASV_331 
## 0.6490206 0.6603731 0.6714038 0.6824268 0.6925248 0.7026192 
## 
## $`1_21`
##     ASV_1     ASV_2    ASV_30    ASV_38     ASV_5    ASV_18 
## 0.2707752 0.4089981 0.5381533 0.6011320 0.6640417 0.7110939

##tank 2c # Beta Diversity and Hierachical clustering tank 2c & similarity percentages (SIMPER)

## phyloseq-class experiment-level object
## otu_table()   OTU Table:         [ 2268 taxa and 45 samples ]
## sample_data() Sample Data:       [ 45 samples by 17 sample variables ]
## tax_table()   Taxonomy Table:    [ 2268 taxa by 7 taxonomic ranks ]
## phy_tree()    Phylogenetic Tree: [ 2268 tips and 2267 internal nodes ]

## 
## Call:
## adonis(formula = final_ps_bray ~ Sampling_day + Fish_ID, data = sampledf) 
## 
## Permutation: free
## Number of permutations: 999
## 
## Terms added sequentially (first to last)
## 
##              Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)   
## Sampling_day  6    2.5936 0.43227  1.3897 0.17931  0.004 **
## Fish_ID       1    0.3617 0.36166  1.1627 0.02500  0.199   
## Residuals    37   11.5090 0.31105         0.79568          
## Total        44   14.4642                 1.00000          
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##  [1] 3  35 0  1  3  7  21 35 7  35 0  21 35 0  21 0  3  5  0  1  21 3  5  7  0 
## [26] 7  35 0  21 35 0  1  3  5  21 35 0  1  35 0  3  7  21 5  0 
## Levels: 0 1 3 5 7 21 35
##  [1] 0  0  0  0  0  0  0  0  0  0  0  1  1  1  1  3  3  3  3  3  3  5  5  5  5 
## [26] 7  7  7  7  7  21 21 21 21 21 21 21 35 35 35 35 35 35 35 35
## Levels: 0 1 3 5 7 21 35

## [1] 45 17
## [1] 45 17
## cumulative contributions of most influential species:
## 
## $`5_0`
##     ASV_1     ASV_2     ASV_4    ASV_34    ASV_13     ASV_3    ASV_26    ASV_18 
## 0.2863347 0.4177174 0.4575488 0.4808084 0.5037789 0.5267439 0.5453065 0.5603975 
##     ASV_6    ASV_33    ASV_73    ASV_99     ASV_7   ASV_121   ASV_124    ASV_38 
## 0.5731826 0.5855582 0.5972368 0.6086703 0.6188564 0.6283868 0.6377273 0.6463001 
##   ASV_135   ASV_109   ASV_168   ASV_158    ASV_22   ASV_177   ASV_180   ASV_175 
## 0.6546488 0.6620780 0.6693295 0.6765609 0.6835705 0.6901881 0.6967411 0.7032557 
## 
## $`5_3`
##     ASV_1     ASV_2     ASV_4     ASV_3    ASV_34    ASV_13    ASV_54    ASV_18 
## 0.2811521 0.4792805 0.5171194 0.5530435 0.5754074 0.5971851 0.6130877 0.6277135 
##    ASV_33    ASV_73     ASV_6    ASV_99     ASV_7   ASV_121   ASV_124   ASV_135 
## 0.6407125 0.6523876 0.6636399 0.6739221 0.6832298 0.6915591 0.6998251 0.7072800 
## 
## $`5_35`
##     ASV_1     ASV_2     ASV_4    ASV_13    ASV_34     ASV_7    ASV_18    ASV_33 
## 0.2566195 0.4093402 0.4605237 0.4848168 0.5079875 0.5273662 0.5424352 0.5547759 
##     ASV_6    ASV_73    ASV_99    ASV_20   ASV_121   ASV_124   ASV_135   ASV_109 
## 0.5664715 0.5779022 0.5885554 0.5978045 0.6064343 0.6149985 0.6227223 0.6296768 
##    ASV_22   ASV_138   ASV_168   ASV_158    ASV_28   ASV_177    ASV_12   ASV_175 
## 0.6365707 0.6433622 0.6501043 0.6567006 0.6630114 0.6691043 0.6751795 0.6811920 
##   ASV_180    ASV_21   ASV_163   ASV_174 
## 0.6871882 0.6929265 0.6985218 0.7040868 
## 
## $`5_1`
##     ASV_1     ASV_2     ASV_9     ASV_4    ASV_34    ASV_13    ASV_10    ASV_33 
## 0.3254215 0.4456450 0.4885336 0.5220691 0.5482736 0.5741326 0.5956718 0.6127300 
##    ASV_18     ASV_5     ASV_6    ASV_73    ASV_99     ASV_7   ASV_121 
## 0.6297862 0.6434871 0.6568051 0.6693703 0.6814183 0.6918865 0.7016461 
## 
## $`5_7`
##     ASV_1     ASV_2     ASV_3     ASV_6     ASV_8    ASV_65     ASV_4    ASV_34 
## 0.2177764 0.3093163 0.3576529 0.3988430 0.4369119 0.4627252 0.4870969 0.5072371 
##    ASV_62    ASV_13    ASV_23    ASV_18    ASV_24    ASV_33    ASV_73    ASV_99 
## 0.5265178 0.5453346 0.5622924 0.5791065 0.5910017 0.6020766 0.6114704 0.6202306 
##     ASV_7   ASV_121   ASV_124   ASV_135   ASV_283    ASV_46   ASV_222    ASV_22 
## 0.6285496 0.6356460 0.6426885 0.6490399 0.6552719 0.6610221 0.6667384 0.6724309 
##   ASV_109   ASV_168   ASV_158   ASV_177   ASV_175   ASV_180 
## 0.6781173 0.6836614 0.6890857 0.6940959 0.6990401 0.7039709 
## 
## $`5_21`
##     ASV_1    ASV_11     ASV_2     ASV_6     ASV_4     ASV_7    ASV_34    ASV_13 
## 0.2907495 0.3876640 0.4837355 0.5202260 0.5550303 0.5785131 0.5983734 0.6177698 
##    ASV_24    ASV_21    ASV_23    ASV_18    ASV_33    ASV_22    ASV_32 
## 0.6335672 0.6490992 0.6631434 0.6766345 0.6881784 0.6995195 0.7091178 
## 
## $`0_3`
##     ASV_1     ASV_2     ASV_3     ASV_4    ASV_54    ASV_26    ASV_38    ASV_12 
## 0.3331047 0.5407862 0.5919523 0.6240325 0.6423142 0.6602689 0.6701381 0.6765544 
##     ASV_6    ASV_14    ASV_28    ASV_66     ASV_9 
## 0.6827531 0.6882556 0.6934419 0.6984788 0.7034621 
## 
## $`0_35`
##     ASV_1     ASV_2     ASV_4     ASV_3    ASV_26     ASV_7    ASV_20    ASV_38 
## 0.3060405 0.4647875 0.5111045 0.5368208 0.5578039 0.5738752 0.5839646 0.5926509 
##    ASV_13    ASV_28   ASV_138    ASV_17    ASV_35    ASV_12    ASV_21    ASV_55 
## 0.6013105 0.6093589 0.6162668 0.6229265 0.6295575 0.6358953 0.6421246 0.6480522 
##   ASV_163   ASV_174    ASV_54   ASV_169    ASV_50    ASV_57    ASV_74    ASV_66 
## 0.6537647 0.6594250 0.6650500 0.6705909 0.6758758 0.6810917 0.6862700 0.6913843 
##     ASV_9    ASV_39 
## 0.6963461 0.7011135 
## 
## $`0_1`
##     ASV_1     ASV_2     ASV_9     ASV_3    ASV_26    ASV_10     ASV_4     ASV_5 
## 0.3424293 0.4903331 0.5406132 0.5720328 0.5945095 0.6167669 0.6363220 0.6505145 
##    ASV_33    ASV_38    ASV_53    ASV_55    ASV_98    ASV_54 
## 0.6624049 0.6731061 0.6810986 0.6889641 0.6959738 0.7029035 
## 
## $`0_7`
##     ASV_1     ASV_2     ASV_3     ASV_6     ASV_8    ASV_65    ASV_62    ASV_23 
## 0.2802434 0.3801416 0.4370157 0.4750818 0.5123121 0.5375614 0.5564209 0.5728002 
##    ASV_26     ASV_4    ASV_24    ASV_18    ASV_38   ASV_283   ASV_222    ASV_46 
## 0.5871904 0.6008452 0.6125437 0.6220539 0.6289228 0.6350185 0.6406098 0.6460915 
##    ASV_13    ASV_54    ASV_32   ASV_106    ASV_66    ASV_55     ASV_9   ASV_110 
## 0.6511950 0.6556432 0.6599976 0.6640486 0.6680990 0.6720405 0.6759462 0.6797125 
##    ASV_20    ASV_74   ASV_156    ASV_12   ASV_436    ASV_57 
## 0.6834613 0.6871129 0.6906038 0.6940843 0.6975428 0.7009974 
## 
## $`0_21`
##     ASV_1     ASV_2    ASV_11     ASV_6     ASV_4     ASV_7     ASV_3    ASV_24 
## 0.3193772 0.4230103 0.5204406 0.5545395 0.5861405 0.6073487 0.6269916 0.6431863 
##    ASV_21    ASV_26    ASV_23    ASV_32    ASV_22 
## 0.6590680 0.6745847 0.6887856 0.6980894 0.7072141 
## 
## $`3_35`
##     ASV_1     ASV_2     ASV_4     ASV_3    ASV_54     ASV_7    ASV_20    ASV_13 
## 0.3086428 0.5324892 0.5777766 0.6158639 0.6318724 0.6467676 0.6554211 0.6637356 
##    ASV_12   ASV_138    ASV_28    ASV_14   ASV_163   ASV_174 
## 0.6714135 0.6780122 0.6841026 0.6901742 0.6956107 0.7010177 
## 
## $`3_1`
##     ASV_1     ASV_2     ASV_3     ASV_9     ASV_4    ASV_10 
## 0.3585911 0.5900502 0.6337019 0.6763147 0.6991655 0.7180738 
## 
## $`3_7`
##     ASV_1     ASV_2     ASV_3     ASV_6     ASV_8    ASV_65    ASV_62     ASV_4 
## 0.2597132 0.4310583 0.4941593 0.5313953 0.5681842 0.5932780 0.6119125 0.6286272 
##    ASV_23    ASV_54    ASV_24    ASV_18   ASV_283   ASV_222    ASV_46    ASV_13 
## 0.6448242 0.6579188 0.6692052 0.6782630 0.6842861 0.6898108 0.6952151 0.7004346 
## 
## $`3_21`
##     ASV_1     ASV_2    ASV_11     ASV_6     ASV_3     ASV_4     ASV_7    ASV_24 
## 0.3064782 0.4897820 0.5834767 0.6162513 0.6471451 0.6776635 0.6978721 0.7131751 
## 
## $`35_1`
##     ASV_1     ASV_2     ASV_9     ASV_4    ASV_10     ASV_7     ASV_5    ASV_33 
## 0.3243739 0.4814258 0.5271135 0.5714108 0.5912203 0.6090764 0.6235757 0.6350782 
##    ASV_20    ASV_13     ASV_3   ASV_138   ASV_163    ASV_98   ASV_174    ASV_28 
## 0.6460756 0.6561994 0.6653436 0.6735166 0.6802501 0.6869777 0.6936747 0.7001074 
## 
## $`35_7`
##     ASV_1     ASV_2     ASV_3     ASV_6     ASV_8     ASV_4    ASV_65    ASV_62 
## 0.2585903 0.3652670 0.4132635 0.4500226 0.4867535 0.5164493 0.5413672 0.5599793 
##    ASV_23     ASV_7    ASV_24    ASV_13    ASV_18    ASV_20   ASV_283   ASV_222 
## 0.5760550 0.5887461 0.6002547 0.6094974 0.6186659 0.6257401 0.6317559 0.6372740 
##   ASV_138    ASV_46   ASV_163   ASV_174    ASV_12    ASV_28   ASV_169    ASV_17 
## 0.6426651 0.6479127 0.6523542 0.6567717 0.6611422 0.6653940 0.6696259 0.6735632 
##   ASV_106    ASV_21   ASV_110    ASV_32   ASV_196   ASV_197   ASV_285     ASV_5 
## 0.6774064 0.6811376 0.6848546 0.6885637 0.6920173 0.6954563 0.6988783 0.7022968 
## 
## $`35_21`
##     ASV_1     ASV_2    ASV_11     ASV_4     ASV_6     ASV_7    ASV_21    ASV_24 
## 0.3105766 0.4201073 0.5174341 0.5600277 0.5931585 0.6205068 0.6369084 0.6528893 
##    ASV_23    ASV_22    ASV_32    ASV_20    ASV_82 
## 0.6668542 0.6761028 0.6849505 0.6936931 0.7022899 
## 
## $`1_7`
##     ASV_1     ASV_2     ASV_3     ASV_8     ASV_6     ASV_9    ASV_65    ASV_62 
## 0.3410236 0.4196907 0.4713634 0.5112571 0.5511474 0.5837744 0.6109316 0.6311847 
##    ASV_23    ASV_10    ASV_24     ASV_5    ASV_18    ASV_33 
## 0.6485407 0.6626849 0.6748369 0.6850610 0.6949047 0.7021033 
## 
## $`1_21`
##     ASV_1    ASV_11     ASV_2     ASV_6     ASV_9     ASV_4     ASV_7    ASV_24 
## 0.3602850 0.4706084 0.5544941 0.5920171 0.6292908 0.6545353 0.6781983 0.6962114 
##    ASV_21 
## 0.7133035 
## 
## $`7_21`
##     ASV_1    ASV_11     ASV_2     ASV_6     ASV_3     ASV_8    ASV_65     ASV_4 
## 0.2653252 0.3495644 0.4147984 0.4648629 0.5084955 0.5431914 0.5667289 0.5861158 
##    ASV_23    ASV_24     ASV_7    ASV_62    ASV_21    ASV_18    ASV_32    ASV_22 
## 0.6054640 0.6246345 0.6429655 0.6605479 0.6736087 0.6838193 0.6928866 0.7008214

##tank 3b # Beta Diversity and Hierachical clustering tank 3b & similarity percentages (SIMPER)

## phyloseq-class experiment-level object
## otu_table()   OTU Table:         [ 1788 taxa and 43 samples ]
## sample_data() Sample Data:       [ 43 samples by 17 sample variables ]
## tax_table()   Taxonomy Table:    [ 1788 taxa by 7 taxonomic ranks ]
## phy_tree()    Phylogenetic Tree: [ 1788 tips and 1787 internal nodes ]

## 
## Call:
## adonis(formula = final_ps_bray ~ Sampling_day + Fish_ID, data = sampledf) 
## 
## Permutation: free
## Number of permutations: 999
## 
## Terms added sequentially (first to last)
## 
##              Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)    
## Sampling_day  6    3.2857 0.54761  1.8083 0.23038  0.001 ***
## Fish_ID       1    0.3771 0.37715  1.2454 0.02644  0.142    
## Residuals    35   10.5989 0.30282         0.74317           
## Total        42   14.2617                 1.00000           
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

## cumulative contributions of most influential species:
## 
## $`0_1`
##     ASV_2     ASV_1     ASV_8    ASV_11     ASV_3     ASV_7     ASV_4    ASV_37 
## 0.1899658 0.3216521 0.3904139 0.4446404 0.4850127 0.5201208 0.5500915 0.5785007 
##    ASV_14    ASV_13     ASV_9     ASV_6    ASV_41    ASV_21   ASV_107    ASV_29 
## 0.6009140 0.6229622 0.6421749 0.6589597 0.6732703 0.6850165 0.6947209 0.7042558 
## 
## $`0_3`
##     ASV_2     ASV_1     ASV_8     ASV_3    ASV_11    ASV_41     ASV_5    ASV_14 
## 0.1559092 0.2493925 0.3120212 0.3469385 0.3763396 0.4001384 0.4230282 0.4418947 
##    ASV_13     ASV_4     ASV_7     ASV_6   ASV_143    ASV_37   ASV_295    ASV_74 
## 0.4591820 0.4753803 0.4906218 0.5033763 0.5156251 0.5253461 0.5347415 0.5433613 
##   ASV_595    ASV_21   ASV_108    ASV_93    ASV_12   ASV_280    ASV_48    ASV_25 
## 0.5515659 0.5596323 0.5676049 0.5745665 0.5810373 0.5867747 0.5921312 0.5974654 
##   ASV_103    ASV_46    ASV_80   ASV_105    ASV_19   ASV_191   ASV_395    ASV_56 
## 0.6021234 0.6062252 0.6101371 0.6140439 0.6177333 0.6213059 0.6248227 0.6282580 
##   ASV_571    ASV_51    ASV_43   ASV_596   ASV_912   ASV_622   ASV_378   ASV_457 
## 0.6315415 0.6348044 0.6379717 0.6410716 0.6441469 0.6470837 0.6500205 0.6529518 
##   ASV_277   ASV_542   ASV_202   ASV_160   ASV_239    ASV_29   ASV_161   ASV_676 
## 0.6558080 0.6586233 0.6613988 0.6641647 0.6668042 0.6694124 0.6719872 0.6745569 
##   ASV_288   ASV_442   ASV_702   ASV_367    ASV_86  ASV_1087   ASV_286   ASV_721 
## 0.6770678 0.6795151 0.6819421 0.6843573 0.6867722 0.6891790 0.6915594 0.6938843 
##   ASV_590   ASV_733   ASV_547 
## 0.6961563 0.6984201 0.7006448 
## 
## $`0_5`
##     ASV_1     ASV_2     ASV_3    ASV_15    ASV_41    ASV_35    ASV_11    ASV_43 
## 0.1596402 0.2769144 0.3660115 0.4096160 0.4458896 0.4776920 0.5074776 0.5333649 
##    ASV_14   ASV_290    ASV_13     ASV_4     ASV_7     ASV_6    ASV_37     ASV_5 
## 0.5525083 0.5715078 0.5889538 0.6046459 0.6195116 0.6324838 0.6426873 0.6505407 
##    ASV_21    ASV_93   ASV_884    ASV_47   ASV_206    ASV_12   ASV_192    ASV_46 
## 0.6582921 0.6653665 0.6721461 0.6776372 0.6828789 0.6873721 0.6916158 0.6957841 
##   ASV_268   ASV_302 
## 0.6997072 0.7035527 
## 
## $`0_7`
##     ASV_1     ASV_2     ASV_3    ASV_11    ASV_14    ASV_13     ASV_8     ASV_4 
## 0.3638775 0.5050852 0.5453576 0.5786506 0.6000419 0.6195454 0.6370942 0.6546343 
##     ASV_7    ASV_41     ASV_6 
## 0.6712497 0.6860534 0.7005586 
## 
## $`0_21`
##     ASV_1     ASV_2     ASV_3    ASV_15    ASV_41    ASV_11    ASV_14    ASV_13 
## 0.2439092 0.3713429 0.4107600 0.4455105 0.4801039 0.5123250 0.5330289 0.5519011 
##     ASV_4     ASV_5     ASV_7    ASV_37     ASV_6    ASV_21   ASV_563    ASV_93 
## 0.5688735 0.5849634 0.6010376 0.6169260 0.6309642 0.6393475 0.6476806 0.6553317 
##    ASV_77    ASV_75    ASV_25    ASV_84    ASV_90   ASV_101   ASV_774 
## 0.6629557 0.6705305 0.6775874 0.6842098 0.6902303 0.6961905 0.7015975 
## 
## $`0_35`
##     ASV_1     ASV_2     ASV_3    ASV_11    ASV_25    ASV_14    ASV_13     ASV_4 
## 0.3160318 0.4524028 0.4918565 0.5249752 0.5558200 0.5771055 0.5965077 0.6139569 
##    ASV_15     ASV_7    ASV_41     ASV_6    ASV_43    ASV_37     ASV_5 
## 0.6307615 0.6472906 0.6617923 0.6762249 0.6883021 0.6992860 0.7083899 
## 
## $`1_3`
##     ASV_2     ASV_8     ASV_1     ASV_7    ASV_11    ASV_41     ASV_5    ASV_37 
## 0.1953861 0.3028605 0.3882193 0.4165535 0.4426971 0.4654072 0.4878189 0.5092063 
##     ASV_9     ASV_4   ASV_143   ASV_295   ASV_107    ASV_74    ASV_12   ASV_595 
## 0.5284794 0.5475480 0.5611506 0.5729895 0.5825308 0.5920093 0.6011954 0.6103068 
##   ASV_108    ASV_29    ASV_13    ASV_28     ASV_6   ASV_280    ASV_48    ASV_22 
## 0.6189996 0.6276851 0.6362907 0.6439800 0.6504982 0.6567543 0.6627028 0.6684749 
##   ASV_112    ASV_25    ASV_44    ASV_21    ASV_19    ASV_14 
## 0.6741686 0.6798234 0.6853675 0.6908227 0.6961823 0.7015123 
## 
## $`1_5`
##     ASV_2     ASV_1     ASV_3     ASV_8    ASV_15    ASV_35    ASV_41    ASV_43 
## 0.1758637 0.3232713 0.3914464 0.4565280 0.5022665 0.5351720 0.5644499 0.5918955 
##     ASV_7    ASV_11    ASV_37   ASV_290     ASV_9 
## 0.6176456 0.6426026 0.6632736 0.6830943 0.7014978 
## 
## $`1_7`
##     ASV_1     ASV_2     ASV_8     ASV_7 
## 0.3923688 0.5839276 0.6703706 0.7009005 
## 
## $`1_21`
##     ASV_1     ASV_2     ASV_8    ASV_15    ASV_41     ASV_7    ASV_11    ASV_37 
## 0.2452798 0.4185032 0.4950443 0.5334728 0.5692247 0.5985179 0.6269086 0.6540209 
##     ASV_9     ASV_4     ASV_5 
## 0.6761574 0.6957824 0.7074032 
## 
## $`1_35`
##     ASV_1     ASV_2     ASV_8    ASV_25     ASV_7    ASV_11    ASV_37 
## 0.3289997 0.5113005 0.5884027 0.6221849 0.6526897 0.6822548 0.7064413 
## 
## $`3_5`
##     ASV_1     ASV_2     ASV_3     ASV_8    ASV_15    ASV_41    ASV_35    ASV_43 
## 0.1354159 0.2632723 0.3262863 0.3875957 0.4295800 0.4694661 0.4998048 0.5245169 
##     ASV_5   ASV_290   ASV_143   ASV_295    ASV_74   ASV_595   ASV_108   ASV_884 
## 0.5433889 0.5616783 0.5736603 0.5828478 0.5911394 0.5991652 0.6068150 0.6133412 
##    ASV_12   ASV_280    ASV_47    ASV_48    ASV_25   ASV_206   ASV_103   ASV_192 
## 0.6191171 0.6246384 0.6299071 0.6351469 0.6402671 0.6452997 0.6497959 0.6541620 
##    ASV_80   ASV_105   ASV_268   ASV_302   ASV_123   ASV_191   ASV_162   ASV_571 
## 0.6579990 0.6617961 0.6655726 0.6692926 0.6728606 0.6763398 0.6796543 0.6828663 
##   ASV_333    ASV_19   ASV_596   ASV_324   ASV_202   ASV_622 
## 0.6860621 0.6892236 0.6922560 0.6952681 0.6981681 0.7010409 
## 
## $`3_7`
##     ASV_1     ASV_2     ASV_8    ASV_41     ASV_5   ASV_143    ASV_15   ASV_295 
## 0.3847470 0.5278730 0.5984213 0.6190516 0.6395609 0.6519637 0.6635236 0.6730590 
##    ASV_74   ASV_595   ASV_108    ASV_20 
## 0.6816860 0.6900158 0.6979523 0.7052822 
## 
## $`3_21`
##     ASV_1     ASV_2     ASV_8    ASV_41    ASV_15     ASV_5   ASV_143   ASV_295 
## 0.2551226 0.3825979 0.4491097 0.4841839 0.5175521 0.5403000 0.5532157 0.5631301 
##    ASV_74    ASV_25   ASV_595    ASV_75    ASV_77   ASV_108   ASV_563    ASV_84 
## 0.5721107 0.5807859 0.5894468 0.5980167 0.6065245 0.6147941 0.6227978 0.6302389 
##    ASV_37    ASV_90   ASV_101   ASV_105    ASV_12   ASV_280   ASV_117    ASV_48 
## 0.6370426 0.6438388 0.6504915 0.6569526 0.6629932 0.6689257 0.6747475 0.6803654 
##   ASV_119   ASV_774   ASV_127   ASV_103 
## 0.6859122 0.6911055 0.6962877 0.7012021 
## 
## $`3_35`
##     ASV_1     ASV_2     ASV_8    ASV_25    ASV_41     ASV_5    ASV_15   ASV_143 
## 0.3379849 0.4693596 0.5341328 0.5594090 0.5804469 0.5997972 0.6152378 0.6278968 
##    ASV_43   ASV_295    ASV_74   ASV_595   ASV_108    ASV_20   ASV_280    ASV_12 
## 0.6380531 0.6477597 0.6565787 0.6650580 0.6731471 0.6803829 0.6861910 0.6917535 
##    ASV_48    ASV_64 
## 0.6972893 0.7023603 
## 
## $`5_7`
##     ASV_1     ASV_2     ASV_3    ASV_15    ASV_35    ASV_41    ASV_43 
## 0.3401562 0.4679233 0.5512435 0.6037216 0.6440680 0.6812394 0.7147328 
## 
## $`5_21`
##     ASV_1     ASV_2     ASV_3    ASV_41    ASV_15    ASV_35    ASV_43   ASV_290 
## 0.2356434 0.3355258 0.4160595 0.4747834 0.5300460 0.5688651 0.6010316 0.6244334 
##     ASV_5   ASV_563    ASV_77    ASV_75   ASV_884    ASV_25    ASV_37    ASV_84 
## 0.6369174 0.6464076 0.6550903 0.6637170 0.6720674 0.6801164 0.6880977 0.6956398 
##    ASV_90 
## 0.7024963 
## 
## $`5_35`
##     ASV_1     ASV_2     ASV_3    ASV_15    ASV_35    ASV_43    ASV_41    ASV_25 
## 0.3057972 0.4266802 0.5112698 0.5643554 0.6051066 0.6429414 0.6795083 0.7152297 
## 
## $`7_21`
##     ASV_1     ASV_2    ASV_41    ASV_15     ASV_8     ASV_5   ASV_563    ASV_77 
## 0.3399139 0.5154741 0.5737377 0.6270493 0.6616425 0.6804544 0.6952852 0.7088542 
## 
## $`7_35`
##     ASV_1     ASV_2    ASV_25     ASV_8 
## 0.3488067 0.6023353 0.6758181 0.7163741 
## 
## $`21_35`
##     ASV_1     ASV_2    ASV_41    ASV_15    ASV_25     ASV_5    ASV_43   ASV_563 
## 0.3096708 0.4555386 0.5107610 0.5639702 0.6116831 0.6305893 0.6487705 0.6629220 
##    ASV_77    ASV_75    ASV_37 
## 0.6758696 0.6887334 0.7007630

##tank 3c # Beta Diversity and Hierachical clustering tank 3c & similarity percentages (SIMPER)

## 
## Call:
## adonis(formula = final_ps_bray ~ Sampling_day + Fish_ID, data = sampledf) 
## 
## Permutation: free
## Number of permutations: 999
## 
## Terms added sequentially (first to last)
## 
##              Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)    
## Sampling_day  6    2.9511 0.49186  1.6938 0.21770  0.001 ***
## Fish_ID       1    0.4413 0.44132  1.5198 0.03256  0.022 *  
## Residuals    35   10.1635 0.29039         0.74974           
## Total        42   13.5560                 1.00000           
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##  [1] 0  0  0  0  0  0  0  0  1  1  1  1  1  3  3  3  3  3  3  5  5  5  5  5  5 
## [26] 7  7  7  7  7  7  21 21 21 21 21 21 21 35 35 35 35 35
## Levels: 0 1 3 5 7 21 35

## [1]   43 1021
## [1] 43 17
## [1] 43 17
## cumulative contributions of most influential species:
## 
## $`0_1`
##     ASV_1     ASV_3     ASV_2     ASV_7     ASV_4    ASV_10    ASV_27    ASV_36 
## 0.1843219 0.3063645 0.4185268 0.4828998 0.5386187 0.5919498 0.6410502 0.6696057 
##     ASV_5     ASV_6 
## 0.6959016 0.7171252 
## 
## $`0_3`
##     ASV_1     ASV_2     ASV_7     ASV_4    ASV_41    ASV_10    ASV_15     ASV_9 
## 0.2347052 0.3084465 0.3736001 0.4299581 0.4792767 0.5271546 0.5718236 0.6066422 
##     ASV_5   ASV_290     ASV_6    ASV_21     ASV_3 
## 0.6347586 0.6554449 0.6758527 0.6956885 0.7140231 
## 
## $`0_5`
##     ASV_1    ASV_15     ASV_2    ASV_41     ASV_7     ASV_4    ASV_10     ASV_5 
## 0.1843774 0.3227982 0.4430433 0.5002742 0.5479178 0.5890501 0.6227381 0.6416406 
##     ASV_6    ASV_21     ASV_3   ASV_613    ASV_14 
## 0.6565899 0.6710815 0.6855019 0.6994655 0.7116222 
## 
## $`0_7`
##     ASV_1     ASV_2     ASV_7     ASV_4    ASV_10    ASV_69     ASV_5    ASV_58 
## 0.3462517 0.4364703 0.4978136 0.5508450 0.5942198 0.6366886 0.6598294 0.6819491 
##   ASV_172 
## 0.7017261 
## 
## $`0_21`
##     ASV_1     ASV_2     ASV_7     ASV_4    ASV_10     ASV_5    ASV_31 
## 0.4165823 0.4974243 0.5637314 0.6210540 0.6679291 0.6927811 0.7163749 
## 
## $`0_35`
##     ASV_1     ASV_2     ASV_7     ASV_3     ASV_4    ASV_10     ASV_9     ASV_5 
## 0.2194957 0.3390156 0.4040006 0.4611365 0.5173163 0.5632718 0.5979512 0.6226659 
##    ASV_17     ASV_6    ASV_21    ASV_14 
## 0.6438854 0.6643603 0.6841266 0.7012104 
## 
## $`1_3`
##     ASV_1     ASV_3     ASV_2    ASV_27    ASV_41    ASV_15     ASV_9    ASV_10 
## 0.1960699 0.3196556 0.4403038 0.4926174 0.5399117 0.5863423 0.6222812 0.6549650 
##    ASV_36   ASV_290 
## 0.6855713 0.7077207 
## 
## $`1_5`
##     ASV_1     ASV_2    ASV_15     ASV_3    ASV_41    ASV_27    ASV_10    ASV_36 
## 0.1854246 0.3275673 0.4681287 0.5539115 0.6139536 0.6501457 0.6720877 0.6932479 
##   ASV_613 
## 0.7074061 
## 
## $`1_7`
##     ASV_1     ASV_2     ASV_3    ASV_27    ASV_69    ASV_10 
## 0.3442872 0.4715041 0.5836696 0.6312931 0.6752980 0.7047229 
## 
## $`1_21`
##     ASV_1     ASV_2     ASV_3    ASV_27 
## 0.4083423 0.5378712 0.6577839 0.7087125 
## 
## $`1_35`
##     ASV_1     ASV_3     ASV_2    ASV_27     ASV_9    ASV_10    ASV_36    ASV_17 
## 0.1825084 0.3383051 0.4867232 0.5416513 0.5796768 0.6136729 0.6457874 0.6697269 
##    ASV_14    ASV_68 
## 0.6869210 0.7037464 
## 
## $`3_5`
##     ASV_1    ASV_15     ASV_2    ASV_41     ASV_9   ASV_290   ASV_613   ASV_113 
## 0.2550408 0.3996110 0.5239419 0.6045151 0.6284162 0.6455828 0.6614439 0.6752702 
##   ASV_495   ASV_848     ASV_5 
## 0.6871647 0.6964440 0.7047446 
## 
## $`3_7`
##     ASV_1     ASV_2    ASV_69    ASV_41    ASV_15     ASV_9    ASV_58   ASV_172 
## 0.3354193 0.4411649 0.4975079 0.5519658 0.6015560 0.6375958 0.6669382 0.6931776 
##   ASV_290 
## 0.7189947 
## 
## $`3_21`
##     ASV_1     ASV_2    ASV_15    ASV_41     ASV_9    ASV_31   ASV_290 
## 0.3739827 0.4673603 0.5339512 0.5976185 0.6432654 0.6779688 0.7081700 
## 
## $`3_35`
##     ASV_1     ASV_2     ASV_3     ASV_9    ASV_15    ASV_41    ASV_17   ASV_290 
## 0.2344869 0.3822032 0.4387048 0.4940174 0.5464978 0.5975971 0.6223389 0.6463747 
##   ASV_113   ASV_305    ASV_68 
## 0.6657336 0.6832495 0.7007528 
## 
## $`5_7`
##     ASV_1    ASV_15     ASV_2    ASV_41    ASV_69    ASV_58 
## 0.3283242 0.4717843 0.5933095 0.6576198 0.6932746 0.7118302 
## 
## $`5_21`
##     ASV_1    ASV_15     ASV_2    ASV_41 
## 0.3897932 0.5475185 0.6543034 0.7205945 
## 
## $`5_35`
##     ASV_1     ASV_2    ASV_15    ASV_41     ASV_3     ASV_9    ASV_17   ASV_613 
## 0.2194831 0.3889882 0.5368303 0.5987786 0.6366637 0.6630294 0.6793146 0.6939320 
##    ASV_68 
## 0.7074731 
## 
## $`7_21`
##     ASV_1     ASV_2    ASV_69    ASV_31    ASV_58 
## 0.3658662 0.5305994 0.6215347 0.6689625 0.7163281 
## 
## $`7_35`
##     ASV_1     ASV_2     ASV_3    ASV_69     ASV_9    ASV_58    ASV_17 
## 0.3633045 0.5217774 0.5760059 0.6265699 0.6654838 0.6918212 0.7156709 
## 
## $`21_35`
##     ASV_1     ASV_2     ASV_3     ASV_9 
## 0.4311703 0.6137946 0.6751535 0.7184669